All sequence reads

Alignments

Alignments for all Neandertal sequences to the human and chimpanzee genomes are available from in BAM format. Download here.

Alignments for all Neandertal sequences to the human and chimpanzee genomes Neandertal reads were mapped to the human genome (hg18), using a custom mapper called ANFO (http://bioinf.eva.mpg.de/anfo). This custom alignment program was developed to take the characteristics of ancient DNA into account. Following the observation and implementation by Briggs et al. {Briggs, 2009 Science}, ANFO uses different substitution matrices for DNA thought to be double stranded versus single stranded and changes between them if doing so affords a better score.

For each library, consensus sequences were constructed from multiple reads of the same Neandertal molecule, defined as having the same orientation, read length, alignment length, and alignment start coordinates. All such clusters, regardless of their mapping quality, are replaced by their consensus sequence. For each observed base and each possible original base, we calculated the likelihood of the observation from its quality score. The base with the highest quality score (calculated by dividing each likelihood by the total likelihood) is used as the consensus.